AUTHOR=Chen Nicolas W. G. , Thareau Vincent , Ribeiro Tiago , Magdelenat Ghislaine , Ashfield Tom , Innes Roger W. , Pedrosa-Harand Andrea , Geffroy Valérie 

TITLE=Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.01185

DOI=10.3389/fpls.2018.01185

ISSN=1664-462X

ABSTRACT=<p>Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (<italic>Phaseolus vulgaris</italic>), the <italic>Co-2</italic> anthracnose resistance (<italic>R</italic>) locus corresponds to a cluster of nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant <italic>R</italic> genes. To study the recent evolution of this <italic>R</italic> gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago. <italic>Co-2</italic> is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within <italic>khipu</italic> satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the <italic>Co-2</italic> cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the <italic>Co-2</italic> cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of <italic>R</italic> genes. We propose that chromosome ends could act as <italic>R</italic> gene incubators in many plant genomes.</p>